rs2297328

Variant names:

• chr10-24524398-A-C
• rs2297328
• NM_019590.5:c.2532A>C

Your query was ambiguous. Multiple possible variants found:

• chr10-24524398-A-C
• chr10-24524398-A-G
• chr10-24524398-A-T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_019590.5(KIAA1217):​c.2532A>C​(p.Thr844Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: KIAA1217 NM_019590.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.34
• Publications: 0 publications found

Genes affected

KIAA1217 (HGNC:25428): (KIAA1217) Predicted to be involved in embryonic skeletal system development. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP7: Synonymous conserved (PhyloP=-4.34 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019590.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1217	NM_019590.5	MANE Select	c.2532A>C	p.Thr844Thr	synonymous	Exon 13 of 21	NP_062536.2
	KIAA1217	NM_001282767.2		c.2427A>C	p.Thr809Thr	synonymous	Exon 12 of 19	NP_001269696.1
	KIAA1217	NM_001282768.2		c.2427A>C	p.Thr809Thr	synonymous	Exon 12 of 18	NP_001269697.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1217	ENST00000376454.8	TSL:1 MANE Select	c.2532A>C	p.Thr844Thr	synonymous	Exon 13 of 21	ENSP00000365637.3
	KIAA1217	ENST00000376451.4	TSL:1	c.1581A>C	p.Thr527Thr	synonymous	Exon 8 of 15	ENSP00000365634.2
	KIAA1217	ENST00000376452.7	TSL:1	c.2427A>C	p.Thr809Thr	synonymous	Exon 12 of 19	ENSP00000365635.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0020
DANN	Benign	0.28
PhyloP100		-4.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2297328; hg19: chr10-24813327;